AIMC Topic: Multigene Family
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Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease.
Nature communications
Jul 12, 2021
Modeling human diseases as networks simplify complex multi-cellular processes, helps understand patterns in noisy data that humans cannot find, and thereby improves precision in prediction. Using Inflammatory Bowel Disease (IBD) as an example, here w...
Disease Models, Animal
Mice, Inbred C57BL
Intestinal Mucosa
Mice, Knockout
Animals
Cohort Studies
Mice
Treatment Outcome
Likelihood Functions
Dextran Sulfate
Colitis
Organoids
AMP-Activated Protein Kinases
Multigene Family
Gene Expression Regulation
Humans
Molecular Targeted Therapy
Artificial Intelligence
Machine Learning
Inflammatory Bowel Diseases
Reproducibility of Results
Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact.
Nature communications
Jun 8, 2021
Chromatin architecture plays an important role in gene regulation. Recent advances in super-resolution microscopy have made it possible to measure chromatin 3D structure and transcription in thousands of single cells. However, leveraging these comple...
Machine Learning Reduced Gene/Non-Coding RNA Features That Classify Schizophrenia Patients Accurately and Highlight Insightful Gene Clusters.
International journal of molecular sciences
Mar 25, 2021
RNA-seq has been a powerful method to detect the differentially expressed genes/long non-coding RNAs (lncRNAs) in schizophrenia (SCZ) patients; however, due to overfitting problems differentially expressed targets (DETs) cannot be used properly as bi...
Ensembling of Gene Clusters Utilizing Deep Learning and Protein-Protein Interaction Information.
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2020
Cluster ensemble techniques aim to combine the outputs of multiple clustering algorithms to obtain a single consensus partitioning. The current paper reports about the development of a cluster ensemble based technique combining the concepts of multio...
Cancer classification based on chromatin accessibility profiles with deep adversarial learning model.
PLoS computational biology
Nov 9, 2020
Given the complexity and diversity of the cancer genomics profiles, it is challenging to identify distinct clusters from different cancer types. Numerous analyses have been conducted for this propose. Still, the methods they used always do not direct...
Ab initio GO-based mining for non-tandem-duplicated functional clusters in three model plant diploid genomes.
PloS one
Jun 19, 2020
A functional Non-Tandem Duplicated Cluster (FNTDC) is a group of non-tandem-duplicated genes that are located closer than expected by mere chance and have a role in the same biological function. The identification of secondary-compounds-related FNTDC...
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions.
BMC bioinformatics
Apr 10, 2020
BACKGROUND: Functional enrichment of genes and pathways based on Gene Ontology (GO) has been widely used to describe the results of various -omics analyses. GO terms statistically overrepresented within a set of a large number of genes are typically ...
TSLRF: Two-Stage Algorithm Based on Least Angle Regression and Random Forest in genome-wide association studies.
Scientific reports
Dec 2, 2019
One of the most important tasks in genome-wide association analysis (GWAS) is the detection of single-nucleotide polymorphisms (SNPs) which are related to target traits. With the development of sequencing technology, traditional statistical methods a...
TADKB: Family classification and a knowledge base of topologically associating domains.
BMC genomics
Mar 14, 2019
BACKGROUND: Topologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can obtain family classifications a...
Novel symmetry-based gene-gene dissimilarity measures utilizing Gene Ontology: Application in gene clustering.
Gene
Sep 2, 2018
In recent years DNA microarray technology, leading to the generation of high-volume biological data, has gained significant attention. To analyze this high volume gene-expression data, one such powerful tool is Clustering. For any clustering algorith...
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